My favourites are Rainbow Dash, Applejack and Derpy.
Derpy, (in third place in the top ones), because she made such a huge impact on the fandom itself. Everywhere you look, you're sure to find something to do with Derpy - whether it be the Save-Derpy! campaign, or fanarts or music... she's been such a big loop for many bronies/pegasisters and has helped to produce masses of beautiful work. She's such a big inspiration! And quite frankly, I find it more offensive that they took her OUT than leaving her in, because it seems so much like she's being singled out because of what a few people think (ironic, since the topic of the show itself is friendship and acceptance that comes WITH that friendship)... I mean, what about kids who are /like/ Derpy? How are they supposed to feel about that? They could get the impression that, in everything they do, it will simply result in them getting put "out of the way" or ignored. She simply shot up in my favourites because of the huge difference she made.
Applejack (up in second for in the top places), I love because of her diligence. She's so damn hard-working. Not to sound arrogant (even though I'm probably going to... ^^;...), but she reminds me of me. I work very hard in order to ensure that I can get somewhere in life, just as she works hard to keep her friends happy, and Sweet Apple Acres up and running smoothly. Also, her voice is fantastic, and her song "Raise This Barn" is so dang catchy! She became my second... well, right from the beginning. She always shone to me for some reason, probably because of her honesty and down-to-earth personality.
And Rainbow Dash... omg... she was just ALWAYS my favourite. I have this very bizarre adoration for colours .. so seeing her was a pure delight for me; she was so bright and alive with colour (still is), that I just couldn't contain myself and instantly got attached to her. I also love the fact that she's so confident, and reminds me of me with the NEED to feel confident. Dash has always been one of those characters that I love to play around with in my mind - in terms of scenarios, etc - and her characteristics as a whole package just really remind me of me. She's fantastic! I think, on first appearance, I got attached to her, and she became my favourite, because I'm in love with both colour, and the idea of wings, haha. :3